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Mendel and Darwin are my homeboys
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Treating a Tenure-Track Faculty Position Like Another Postdochttps://collegebiology.wordpress.com/2014/11/13/treating-a-tenure-track-faculty-position-like-another-postdoc/
https://collegebiology.wordpress.com/2014/11/13/treating-a-tenure-track-faculty-position-like-another-postdoc/#respondThu, 13 Nov 2014 14:22:15 +0000http://collegebiology.wordpress.com/?p=180Continue reading →]]>For many postdocs, there’s a lot of tension surrounding the transition to a tenure-track faculty position. And rightfully so since this is one of the most crucial junctures in our academic careers. We ask ourselves, “Will I be able to work at the institution I want? Do I have the credentials? Will I be able to get tenure in 4-7 years? What happens if I don’t?”

A blog post was published last year from Scientific American that aims to upend how we look at starting faculty positions. In her article, “The Awesomest 7-Year Postdoc or: How I Learned to Stop Worrying and Love the Tenure-Track Faculty Life,” Dr. Radhika Nagpal urges us to focus on what matters. An academic faculty position is a dream job for some, so why spend the entire time worrying about meeting the right people, serving on enough committees, and jumping through all of the hoops of what you are supposed to do?

With a few hard-and-fast ground rules, and a supportive family, Dr. Nagpal created work-life balance for herself. She had to prioritize her work, and say no to many opportunities, but she also got to take scientific risks that have paid off. If you’re at all interested in an academic career, or not sure it would be for you, give this article a read.

In a biology or genetics course, students are tasked with learning quantitative ideas such as linkage, recombination, and genetic drift. Up until this point, biology can be heavier on facts and ideas than more numerical subjects such as chemistry and physics. Then, students have to start grappling with multiple sets of information: biology in the form of Mendel, chromosomes, mitosis, meiosis, Punnett squares, etc.; mathematics in the form of measurement, algebra, statistics (Chi-square), and probabilities. Geneticists, like many disciplines, also have their own language and favorite go-to examples. Problems involve wrinkly peas, dwarf plants, bearded dragons, calico cats, and people with hemophilia; test cross, back cross, parental, and filial.

Like most skills, mastering these complex, interdisciplinary ideas comes through practice, practice, and more practice. One of the limiting factors for students may be that their instructors only provide so many opportunities to calculate linkage, fitness, and changing allele frequencies.

Mendelian genetics – up to three genes available for Punnett squares in the Cross Simulator

Gene/trait mapping – calculating linkage

Heritability – using Breeder’s equation

Hardy-Weinberg

Population genetics

Fitness – the Allele Freak feature simulates the possible fates of alleles based on evolutionary influences

Best of all, the app is free! This app is great for students to practice concepts learned in class. It can also be an easy way for instructors to generate homework and test questions with the press of a button. I highly recommend this as a great learning resource.

]]>https://collegebiology.wordpress.com/2014/09/16/genetics-and-evolution-app/feed/0collegebiologyGenEvolAppTranscription & Translation Practice with the RandomORF Generatorhttps://collegebiology.wordpress.com/2014/09/02/transcription-translation-practice-with-the-randomorf-generator/
https://collegebiology.wordpress.com/2014/09/02/transcription-translation-practice-with-the-randomorf-generator/#respondTue, 02 Sep 2014 20:55:32 +0000http://collegebiology.wordpress.com/2014/09/02/transcription-translation-practice-with-the-randomorf-generator/Continue reading →]]>It can be a long and confusing road for students to learn the Central Dogma of Molecular Biology (DNA begets RNA begets protein). Students have to grapple with specifics such as 5′ to 3′, DNA vs. RNA nucleotides, base pairing, triplets, coding vs. template strand, and using a translation chart. If you are not very specific with the questions you ask on assignments or exams, you can receive widely varied answers that are the reverse or complement of the “correct” answer.

In the latest issue of CBE – Life Sciences Education, Carr, et al. provide an explanation for their simplified approach to learning the Central Dogma. Even better, they have created a web application to generate “random” sequences for students to use for practice. The webapp is called RandomORF Generator, as shown below:

Figure depicting RandomORF Generator’s interface. Carr, et al. 2014.

The idea is that students will see an oligomer of some number of base pairs and it is up to them to figure out which of the 6 possible reading frames is the one that will encode a protein. Each of the other 5 reading frames contains a stop codon. The same is true of researchers looking at novel nucleotide sequences. You would have to figure out which open reading frame (ORF) is the one with a biological function without multiple stop codons.

Students can practice on their own using this website. After choosing an oligomer length, the webapp makes a nucleotide sequence. When the student is finished or needs some help, another click shows the 6 different reading frames and which one lacks any stop codons. The webapp could also be used to make assignment or exam questions.

As a side note, I want to share my favorite protein translation codon chart (see below). Many charts are organized into a table, but I find this circular version much easier to handle. The first RNA nucleotide of the codon is in the innermost circle, the second nucleotide in the middle circle, and the last nucleotide (the wobble base) is in the outermost circle. With a little practice, students can pick this chart up pretty quickly.

]]>https://collegebiology.wordpress.com/2014/09/02/transcription-translation-practice-with-the-randomorf-generator/feed/0collegebiologyRandomORF generatorProtein Codon WheelApplying to STEM Graduate School, Parts 2 and 3https://collegebiology.wordpress.com/2014/08/26/applying-to-stem-graduate-school-parts-2-and-3/
https://collegebiology.wordpress.com/2014/08/26/applying-to-stem-graduate-school-parts-2-and-3/#respondTue, 26 Aug 2014 21:47:15 +0000http://collegebiology.wordpress.com/2014/08/26/applying-to-stem-graduate-school-parts-2-and-3/The second and third guest posts on applying to STEM graduate school are now up on Aaron Long’s blog, The Doctoral Road: Part II and Part III. Head over there to learn more!
]]>https://collegebiology.wordpress.com/2014/08/26/applying-to-stem-graduate-school-parts-2-and-3/feed/0collegebiologyTED Talk: Geena Rocero – Why I must come outhttps://collegebiology.wordpress.com/2014/08/26/ted-talk-geena-rocero-why-i-must-come-out/
https://collegebiology.wordpress.com/2014/08/26/ted-talk-geena-rocero-why-i-must-come-out/#respondTue, 26 Aug 2014 21:40:20 +0000http://collegebiology.wordpress.com/2014/08/26/ted-talk-geena-rocero-why-i-must-come-out/Continue reading →]]>Human biology can be a tricky subject. It takes the world of the abstract, with its nondescript cells, mRNA, membrane structures, etc., and puts it into the context of the human experience. Trisomy 21 is no longer a factoid to be remembered, but rather a group of real individuals who have the same feelings and desires as the rest of us. Alzheimer’s starts as a study of neurobiology, but can grow to encompass the difficulties of being a caregiver. While melanocytes may give your skin pigment, the amount of that pigment has had a profound impact on human history that continues today.

It is in this spirit that I share this TED Talk from Geena Rocero. Geena was born biologically male, but she identified as a female. She describes her experiences as a trans woman in this video. What better way to start a discussion on gender identity than to hear a story from this brave woman.

Topics relevant to this video are:

Sex vs. gender

Gender identity

Gender changes in the biological world

Fluidity of human gender and sexuality

Some may say that a video like this is more about social issues and better suited to a humanities classroom. I wholeheartedly disagree. Whenever you can engage with a student on an important subject that is directly related to the curriculum, especially one receiving so much current attention in the media, we as educators have an obligation to explore that topic. We can dispel rumors and create understanding. We may even have trans students in our classrooms that are struggling with their identity. By treating the subject fairly and with compassion, you can go a long way to spreading awareness and open-mindedness.

]]>https://collegebiology.wordpress.com/2014/08/26/ted-talk-geena-rocero-why-i-must-come-out/feed/0collegebiologyApplying to Graduate Programs in STEM, Part 1: The Application Processhttps://collegebiology.wordpress.com/2014/08/05/applying-to-graduate-programs-in-stem-part-1-the-application-process/
https://collegebiology.wordpress.com/2014/08/05/applying-to-graduate-programs-in-stem-part-1-the-application-process/#respondTue, 05 Aug 2014 23:20:14 +0000http://collegebiology.wordpress.com/2014/08/05/applying-to-graduate-programs-in-stem-part-1-the-application-process/Continue reading →]]>I was contacted by fellow blogger Aaron Long of The Doctoral Road to write a series of guest blog posts. The Doctoral Road covers topics on graduate programs in the humanities, and Aaron asked that I give the STEM perspective. To read my post, click here.
]]>https://collegebiology.wordpress.com/2014/08/05/applying-to-graduate-programs-in-stem-part-1-the-application-process/feed/0collegebiologyPoetry in the Science Classroomhttps://collegebiology.wordpress.com/2014/04/27/poetry-in-the-science-classroom/
https://collegebiology.wordpress.com/2014/04/27/poetry-in-the-science-classroom/#respondSun, 27 Apr 2014 22:35:14 +0000http://collegebiology.wordpress.com/?p=167Continue reading →]]>In school, particularly K-12, students spend a lot of their mental power categorizing themselves. Which clique do I fit into? Jocks, nerds, cheerleaders, popular kids, drama dorks, marching band, emos, goths, punks, skateboarders, surfers, or rappers? AP, gifted, average, or failing? Team Edward or Team Jacob?

One false dichotomy that was evident during my course on DNA with Duke TIP: scientist or artist. Of my 16 middle school students, 14 had very strong opinions that they were clearly scientists and had nothing to do with creative ventures. The other two students were the types to dabble in a lot of different subjects, so they understood that this is not an either-or situation.

Clearly, this class, like most of the general public, does not get the chance to see the creativity that goes into science. New technologies and novel ideas are the base materials of high-impact publications. Interdisciplinary science is defined as taking information or techniques from one field and applying them to another. Hence, the birth of biochemistry, molecular evolution, and bioinformatics.

Many of the long-shot, crazy-unless-it-works ideas are never published (let alone publicized) and are called negative data. Even worse, the current tight funding situation has led to fewer innovative grants funded (see Bruce Albert’s comments). Plus, the way science is often taught in schools makes it seem like scientists spend all their time memorizing books of known facts instead of synthesizing new knowledge and solving problems.

Back to my middle school students, their attitudes about science vs. art became so vehement that they would bad-mouth the neighboring creative writing class. Creative writing became the slow gazelle of the entire TIP summer camp. So the creative writing teacher and I did what good teachers do: conspire against the students.

I gave the students a 30 minute assignment: write poetry about DNA. You would have thought I asked them to cut off their right hand. I had to deal with more whining for this assignment than any other from that entire summer. To make the assignment a little more student-friendly for students who didn’t want to worry about rhyming, I offered a perennial favorite of student poetry – the haiku (though since haiku are shorter than other poems, they had to write at least 10). Here are some excerpts of the results:

DNA“…And those pairs are made up of bases
That hold like the knot on your shoe laces.”

Untitled“…When they need to make copies there’s no hesitation
They begin a process called replicationThe double helix is pulled apart by the helicaseThis happens very fast like a race…”

DNA oh DNA“…Molecule of life
with base pair after base paircoding my person”

Untitled“DNA is the start,
Proteins are the end,RNA comes in the middle,A Helicase unbends…”

DNA Haikus #8“We are being usedReplicators control usThe fittest survive”

DNA by Unnamed Teaching Assistant
“It started with Watson and Crick;Molecules muddled ball-and-stick.Base pairs, sugars and phosphates too,hydrogen bonds hold them together like glue.Double helix is the shape of the strands,complimentary like left and right hands.The direction it takes, 5 to 3 prime,which is how we will end this DNA rhyme.”

Each of these poems was reviewed by the creative writing class, who provided excellent constructive criticism in the style of the “feedback sandwich.” Many students reported warming up to writing creatively about science. Plus they had the chance to learn about peer review etiquette.

Does writing creatively have a place in the college classroom? Absolutely. If designed well, a creative assignment asks students to break away from traditional modes of assessment (quizzes, tests, calculations, labs, etc.). Students are forced to synthesize what they know in new combinations. For the instructor, a creative writing assignment may be more useful in assessing how well students understand the material beyond memorization. Plus they are far more entertaining to grade.

]]>https://collegebiology.wordpress.com/2014/04/27/poetry-in-the-science-classroom/feed/0collegebiologyTED Talk: Gabe Garcia-Colombo – My DNA Vending Machinehttps://collegebiology.wordpress.com/2014/03/18/ted-talk-gabe-garcia-colombo/
https://collegebiology.wordpress.com/2014/03/18/ted-talk-gabe-garcia-colombo/#respondWed, 19 Mar 2014 01:44:21 +0000http://collegebiology.wordpress.com/?p=164Continue reading →]]>The worlds of science and art do not always see eye to eye. Many people feel that they are almost mutually exclusive. If you’re artistic, you don’t understand math and science. If you’re a science geek, you don’t have an artistic bone in your body (in addition to the other 206). These fields seem as opposite as protons and electrons or Othello and Iago.

The truth is not so black and white. Creative folks have to employ a knowledge of their materials. STEM nerds need creativity to figure out the hows and whys of the world. One lesson I try to instill in my students is that the scientific method, that dry series of steps we’re forced to memorize since elementary school, is actually how people inherently learn and solve problems.

This post is the first in a series I will write on the subject of creativity in the science classroom. My goal is for students to explore their own creativity and for instructors to see the utility of these types of lessons.

Many of us have extracted DNA from strawberries. Gabe Garcia-Colombo, the artist in the video, was inspired by this process to have DNA extraction parties with his friends. Taking it a step further, he has created a vending machine at which you can purchase a vial of someone else’s DNA.

This video would be a good assignment after a DNA extraction lab, whether from strawberries or from students’ cells. Once they see how easy it is to obtain DNA, a larger impact discussion can occur about genetic rights.

Questions for students:

What did Gabe Garcia-Colombo do after he was inspired by DNA extractions?

Describe the DNA vending machine.

What are some pros for having DNA vending machines? For instance, would the public benefit somehow from these machines?

What are some cons for having DNA vending machines? Could these machines somehow harm the people buying the DNA or the donors supplying the DNA?

Would you buy someone’s DNA out of the vending machine? Would you supply your own? If you would supply your own, would you donate your DNA or ask for some money?

Name 3 things you could do with someone else’s DNA? What resources would you need?

How should ownership of DNA work? Should it be like property or intellectual property?

Students may leap to the possibility of cloning a human from their DNA which may be a discussion for another class. The big ideas that students should recognize is that owning a person’s genetic code is both intimate and limited. It is intimate because that code is present in nearly every cell in that person’s body. But it is also limited in that you have to have access to sequencing technology to decipher the code, and even then our ability to predict phenotypes (traits or medical history) are not very strong at the moment.

Another issue to raise is more nefarious: framing someone with their DNA as evidence. Ask students how this may be achieved and what sort of steps could be taken to avoid this problem.

Gabe Garcia-Colombo’s innovative DNA vending machine raises interesting questions in the burgeoning age of personalized genomics. That’s what a little creativity can do for science.

]]>https://collegebiology.wordpress.com/2014/03/18/ted-talk-gabe-garcia-colombo/feed/0collegebiologyDe-extinction: Resurrecting Lost Specieshttps://collegebiology.wordpress.com/2014/03/02/de-extinction-resurrecting-lost-species/
https://collegebiology.wordpress.com/2014/03/02/de-extinction-resurrecting-lost-species/#respondMon, 03 Mar 2014 01:03:00 +0000http://collegebiology.wordpress.com/?p=161Continue reading →]]>A hot topic in biology is the idea that we could resurrect extinct species. Immediately, most people start to think about Jurassic Park and having a dodo as a pet. Studying the science and ethics of this type of research can help shape students’ attitudes toward ecology and preservation efforts.

One of the major movements in ecology over the past century has been the preservation of species and their habitats. In the 60’s and 70’s, the U.S. Congress passed acts to classify species as threatened, endangered, and extinct, which offered specific legal protections. Many species have been brought back from the edge of extinction through these efforts, such as the bald eagle and grizzly bear.

Image from: Wikipedia

However, these efforts have fallen short for many species including the Pyrenean ibex and the Western black rhinoceros. Classic examples of species that have been hunted to extinction in the past hundred years are the dodo, the Tasmanian tiger (thylacine), and the passenger pigeon. Worse still, habitat destruction and global warming currently threaten much of the world’s biodiversity.

Advances in biotechnology may offer a new hope for resurrecting extinct species. In this first TED Talk, Stewart Brand describes different methods for bringing animals back from the dead.

Some projects use techniques similar to those used to clone Dolly the sheep. Others try to back-breed extant (living), related species to re-create the lost organisms. Brand shares many of the ideas that biologists are currently testing.

Similarly, in the following TED Talk, Michael Archer shares his person experiences in trying to resurrect two (currently) extinct species – the gastric brooding grog and the thylacine. His important successes on the way to bringing these species back make these ideas seem even more real and possible in our lifetimes.

One question that arises from these videos is what will happen to these species once they’ve returned. Will they act the same as their ancestors if they have no parents to teach them? If they exhibit the DNA but not the behaviors of the original animal, does that mean they are a different species altogether? There are no easy answers to these questions, which can make them good fodder for a classroom discussion or a debate.

Another question harkens back to ecology – what impact would reintroducing these species have on their habitats? While the removal of these species would have profoundly impacted their ecosystems, placing the species back in could also have negative effects. After students have seen one or both of the previous videos, this last TED Talk by George Monbiot about this very topic can be a natural extension of the conversation.

According to Monbiot, returning these species could also have beneficial effects and lead to a more balanced ecosystem. Much will depend on the particular species and the context in which it lived, including how it obtained food, what predators it had, and what other species benefited from its existence.

This entire conversation may seem like science fiction, but it is quickly becoming science fact. Recently extinct species may be revived first, depending on the availability of high-quality frozen tissues. As our ability to manipulate genomes improves, we could potentially resurrect species from nothing more than their genetic sequence. Many articles have been published recently about hominid genomes such as Neanderthals. Even if we did not have viable cell samples from these species, we could eventually see our evolutionary cousins on exhibit at the local zoo.

Work such as this has important ethical questions that students should consider. Why should we develop these tools and resurrect species? By that same token, why should we spend time and money to help endangered species?

If you start reviving species, which ones should receive priority? An idea for an assignment would be to ask students to identify one or a few species that they believe would be important to bring back and to justify their choices. You may also ask them to consider the difficulty of resurrection in their choices. A real-life Jurassic Park would be an amazing experience, but it would be extremely difficult to obtain useful biological samples from 65 million-year-old fossilized bones.

What should we do with the species once they have come back? Should there be an ultimate goal, such as reintroduction into the wild? Or is anything possible, including zoos, domestication for agriculture, keeping as pets, hybridizing with other species, etc.?

Resurrecting extinct species has the promise of righting some of mankind’s destructive past and helping to preserve biodiversity. Students can apply their knowledge of biological techniques, genetics, and cell biology to these complex issues. The real world context should also motivate them to generate ideas, formulate opinions, and start to care about matters of ecology.

]]>https://collegebiology.wordpress.com/2014/03/02/de-extinction-resurrecting-lost-species/feed/0collegebiologyImage from: WikipediaTED Talk: Skylar Tibbits – The Emergence of 4D Printinghttps://collegebiology.wordpress.com/2014/03/01/ted-talk-skylar-tibbits-the-emergence-of-4d-printing/
https://collegebiology.wordpress.com/2014/03/01/ted-talk-skylar-tibbits-the-emergence-of-4d-printing/#respondSun, 02 Mar 2014 02:38:57 +0000http://collegebiology.wordpress.com/?p=156Continue reading →]]>In biology, DNA is the blueprint, but it is proteins that are the workhorses of the cell. For the most part, proteins are the components that actually “do” something. They catalyze reactions, give the cell structure, communicate information, haul cargo, and help the cell move.

The idea that proteins can assemble themselves is a difficult one for students to grasp. First, they have to understand that proteins are encoded by a particular sequence of amino acids (genetics, central dogma, cell biology). Next, they need to know that these amino acids interact in particular, semi-predictable ways (biochemistry). Then, the students have to learn that structure determines protein function and changes in structure can alter function (more biochemistry). This combination of details makes proteins a very difficult subject to discuss, particularly with novice students.

Skylar Tibbits gave an excellent TED Talk that can help introduce the idea of “self-assembly” to students. In this talk, Tibbits shows videos of objects made of plastics, such as ones you would obtain from a 3D printer. The difference with Tibbits’ objects is that after they are made, they change conformation on their own. These materials are “pre-programmed” to transform in response to heat, time, or different solutions. The conformational changes almost look like a trick, but as Arthur C. Clarke said, “any sufficiently advanced technology is indistinguishable from magic.” That’s exactly what cells are – a 3.7 billion-year-old technology.

I would recommend first introducing students to translation and protein structure (primary, secondary, tertiary, and quaternary). As you prepare to show the video or assign it for homework, preface it by making the connection to protein self-assembly. These are some possible guiding and reflection questions for students:

What is “self-assembly?” If all products where manufactured to self-assemble, how would that change how factories work? Can you think of examples from your everyday life of objects that you would like to see self-assemble?

What is a benefit of self-assembly for cells? What sort of systems would a cell have to possess if proteins did not self-assemble?

What about a protein determines how it functions? Is this true for proteins that act as enzymes?

What features of a protein do you think enable it to self-assemble?

Would a protein that normally exists embedded in the plasma membrane self-assemble in the same way as a cytosolic protein?

After introducing protein folding and function in this way, you can follow up by showing students this popular video from Harvard: The Inner Life of the Cell. In the video, ribosomes produce proteins that self-assemble and later have particular roles in the cell. Both of these videos can help students understand these complex topics using excellent images of these processes in action.